Halogen Bonds in Adenine-5-Bromouracil Complexes

Ab initio and density functional calculations were employed to investigate the bonding patterns in theadenine-5-bromouracil (AT+) complexes. It is shown that the Br atom in 5-bromouracil (T+) is involved in bonding both with the hydrogen atom of the amino group of adenine (A) and with N7(A) (or N1(A)). With this motif, the Br atom interacts with a nucleophile (H) in a "head-on" fashion and an electrophile(N) in a "side-on" fashion, forming both hydrogen and halogen bonds. Electrostatic attraction between the Br atom in T+ and N7 (or N1) of adenine was found via the electrostatic potential analysis. The existence of the Br···N interactions in the pairs was further conˉrmed by means of Bader's atoms in molecules theory. A bond critical point is identiˉed for the halogen bonds and the topological parameters at the bond critical point indicate the typical closed-shell interactions in the pairs. Natural bond orbital analysis suggests that the charge transfer from the lone pair of the nitrogen atom of adenine is mainly directed to the C-Br antibonding orbital. Finally, halogen bonds in the T+AT+A tetrads were also explored.     

Structure and dynamics of pyrimidine-based macrocycles in solution

The conformational structure of macrocycles obtained from two thiopyrimidine and uracil nucleic acids linked by polymethylene spacers is determined by the length of the spacers, intramolecular NH bonding, pH and solvent. In CDCl₃, NH-OC hydrogen bonding can impact the overall stabilization of the folded conformation, however spatial preorganization to such hydrogen bonding is a prerequisite. Protonation leads to disruption of intramolecular hydrogen bonds, destabilization of the folded conformation and to strong counterion assisted self-aggregation of macrocyles which can be destroyed in polar solvents.     

分子间弱相互作用的计算——构建氢键、卤键势能面

介绍一个面向大三下学期本科生的计算化学实验。通过量子化学计算对比研究两种分子间弱相互作用——氢键和卤键的势能面,使学生对势能面的概念及两种弱相互作用的区别有一定的直观认识。通过实际上机操作,初步了解Gaussian、Gaussview及Origin等计算化学相关软件的使用,并深入理解结构化学及计算化学课程中所学的理论知识。     

Triangular Halogen Bond and Hydrogen Bond Supramolecular Complex Consisting of Carbon Tetrabromide,Halide, and Solvent Molecule： A Theoretical and Spectroscopic Study

The theoretical calculation and spectroscopic experiments indicate a kind of triangular three bonding supramolecular complexes CBr4…X^-…-H-C, which consist of carbon tetrabromide, halide, and protic solvent molecule （referring to dichloromethane, chloroform and acetonitrile）, can be formed in solution. The strength of halogen and hydrogen bonds in the triangular complexes using halide as common acceptor obeys the order of iodide〉bromide〉chloride. The halogen and hydrogen bonds work weak-cooperatively. Charge transfer bands of halogen bonding complexes between CBra and halide are observed in UV-Vis absorption spectroscopy in three solvents, and then the stoichiometry of 1：1, formation constants K and molar extinction coefficients ε of the halogen bonding complexes are obtained by Benesi-Hildebrand method. The K and ε show a dependence on the solvent dielectric constant and, on the whole, obey an order of iodide〉bromide〉chloride in the same solvents. Furthermore, the C-H vibrational frequencies of solvent molecules vary obviously with the addition of halide, which indicates the C-H…X- interaction. The experimental data indicate that the halogen bond and hydrogen bond coexist by sharing a common halide acceptor as predicted by calculation.     

卤键在超分子化学中的应用进展

卤键是指作用在卤原子(路易斯酸)和具有孤对电子的原子或π电子体系(路易斯碱)之间的新型弱相互作用,其在超分子多维自组装和分子识别(如超分子催化、超分子选择拆分、超分子传感)等领域有着广泛的应用。本文介绍了卤键的类别、特性、功能及在超分子化学结构与功能领域中的应用。     

Thiophene and naphthalene-based double helix: Synthesis,structures and chirality

Both racemate and enantiomer of a novel double helix,binaphthylcyclooctaterthiophene(BN-COTh),which is a DNA-like molecule constructed by two single helices intertwined with each other via covalent bonds,have been synthesized with two building blocks,cycloocta-tetrathiophene(COTh) and cyclooctadinaphthyldithiophene(CONT) fused together via Negishi coupling reaction.Another homologue,dinaphthylcyclooctaterthiophene(DN-COTh) has been employed together as a model compound.Besides the synthetic work,BN-COTh and DN-COTh have been investigated by studying their crystal structures,spectroscopic behaviors,chiral resolution and chiral characteristics,including circular dichroism(CD) spectra and optical rotations.In addition,the novel crystal of enantiomer of(R,R,R)-BN-COTh has been explored.The enantiomer molecules packing along b-axis to form a larger and extended assembly packing due to intermolecular interactions between the enantiomer molecules and chloroform molecules in crystal.     

Influence of gelator structures on formation and stability of supramolecular hydrogels

A supramolecular hydrogel(defined as G1) formed from 1,2,4,5-benzene tetracarboxylic acid (BTCA) and 2-amino-3- hydroxypyridine possessed higher T_(gel) than that of another hydrogel(defined as G2) formed from BTCA and 3-hydroxypyridine. Based on the analysis of their xerogels by ~1H NMR,IR and XRD,the higher stability of G1 was attributed to the formation of stronger hydrogen binding enhanced by the ortho amino group of 2-amino-3-hydroxypyridine.     

Formation of double helix self-assembled monolayers of ethynylhelicene oligomer disulfides on gold surfaces

Optically active ethynylhelicene pentamers and hexamers linked by disulfide bonds were synthesized. They formed self-assembled monolayers (SAMs) with double helix structure on gold surfaces, which were analyzed by infrared reflection-absorption spectroscopy (IR-RAS), quartz crystal microbalance (QCM), surface plasmon resonance (SPR), and circular dichroism (CD). Double helix SAMs could be formed on gold surfaces either from double helices or random coils in solution. The double helices on the surface were more stable than in solution. This result suggested the presence of strong intercomplex interactions between double helix complexes on the surface.     

Hydrogen and Halogen Bonding to Au(I) Fluorido Complexes

The hydrogen bonding in the Au(I) complex [Au(F ⋅ HF)(SPhos)] (SPhos=dicyclohexyl(2’,6’-dimethoxy[1,1’-biphenyl]-2-yl)phosphane) ( 1 a ⋅ HF) has been analysed by IR and NMR measurements, revealing the formation of an unsymmetrical bifluoride moiety. The data are in excellent agreement with DFT calculations. Comparisons to analogous complexes bearing NHC (NHC=N-heterocyclic carbene) ligands demonstrated a comparable bonding situation. The identity of the halogen bond in the compound [Au(F ⋅ IC₆F₅)(SPhos)] ( 1 a ⋅ IC₆F₅) in CD₂Cl₂ has been estimated, and van't Hoff data for the equilibrium between [Au(F)(SPhos)] ( 1 a ) and IC₆F₅ with [Au(F ⋅ IC₆F₅)(SPhos)] are ΔH⁰=−8.1(3) kJ mol⁻¹ and ΔS⁰=−36(1) J (mol K)⁻¹. The latter are also in agreement with DFT calculations. For all calculations, comparisons between an explicit and implicit solvent model were drawn. Single crystal X-ray diffraction studies were performed for [Au(F ⋅ 2IC₆F₅)(BrettPhos)] ⋅ 2IC₆F₅ (BrettPhos=2-(dicyclohexylphosphino)-3,6-dimethoxy-2’,4’,6’-triisopropyl-1,1’-biphenyl) ( 1 b ⋅ 4IC₆F₅) demonstrating the presence of halogen bonds to Au(I) fluorido complexes in the solid state.     

Halogen bond preferences of thiocyanate ligand coordinated to Ru(II) via sulphur atom

Halogen bonding between [Ru(bpy)(CO)₂(S-SCN)₂] (bpy = 2,2’-bipyridine), I₂ was studied by co-crystallising the metal compound and diiodine from dichloromethane. The only observed crystalline product was found to be [Ru(bpy)(CO)₂(S-SCN)₂]⋅I₂ with only one NCS⋅⋅⋅I₂ halogen bond between I₂ and the metal coordinated S atom of one of the thiocyanate ligand. The dangling nitrogen atoms were not involved in halogen bonding. However, computational analysis suggests that there are no major energetic differences between the NCS⋅⋅⋅I₂ and SCN⋅⋅⋅I₂ bonding modes. The reason for the observed NCS⋅⋅⋅I₂ mode lies most probably in the more favourable packing effects rather than energetic preferences between NCS⋅⋅⋅I₂ and SCN⋅⋅⋅I₂ contacts.     

Halogen Bonding or Hydrogen Bonding between 2,2,6,6-Tetramethyl-piperidine-noxyl Radical and Trihalomethanes CHX3 (X=Cl,Br, I)

The halogen and hydrogen bonding complexes between 2,2,6,6-tetramethylpiperidine-noxyl and trihalomethanes (CHX₃, X=Cl, Br, I) are simulated by computational quantum chem-istry. The molecular electrostatic potentials, geometrical parameters and interaction energy of halogen and hydrogen bonding complexes combined with natural bond orbital analysis are obtained. The results indicate that both halogen and hydrogen bonding interactions obey the order Cl相似文献   

Reactions of Halogen Azides

Until recently, the explosive nature of halogen azides made these compounds unsuitable for preparative uses and greatly impeded investigation of their physical properties. Reactions of ClN₃ and BrN₃ with metal halides, metal carbonyls, and organometallic compounds to from metal azide halides, nitride halides, carbonyl azide halides, and alkylmetal azides were reported only very recently. The stability relationships of the halogen azides are discussed.     

Hydrogen bonded arylamide-linked cholesteryl dimesogenic liquid crystals: a study of the length and side chain effects

Dimesogenic compounds 1a-c, 2a-i, and 3, that are composed of a hydrogen bonding-induced straight arylamide spacer and two appended cholesterol groups, have been designed and synthesized. The backbones of the rigid spacers of 1a-c, 2a-i, and 3 contain one, three, and five benzene units, which bear two, six, and ten alkoxyl (methoxyl, n-octoxyl, or n-dodecoxyl) groups, respectively. The thermal and optical properties of the compounds are investigated by using the differential scanning calorimetry (DSC), polarizing optical microscopy (POM), and powder X-ray diffraction (PXRD) analysis. It is revealed that 1a-c exhibit one or two liquid crystalline (LC) phases, 2a-i exhibit no, one or two LC phases, while 3 exhibits one LC phase in a wide temperature range. Generally, the more and longer alkoxyl chains facilitate the formation of the LC phases at low temperature. Notably, compound 2g, which bears two methoxyl and four dodecoxyl groups, displays a blue-red color change during both the heating and cooling cycle. The result illustrates that dimesogens with large rigid spacers can exhibit different LC phases when long aliphatic chains are appended to balance the strong stacking of the rigid backbones.     

Hydrogen bonding and halogen bonding co-existing in the reaction of heptafluorobenzyl iodide with N,N,N,N-tetramethylethylene diamine

Two novel assembling systems 3 and 4, with the structures of C₆F₅CF₂⁻?H⁺N(Me)₂CH₂CH₂(Me₂)N⁺H?⁻CF₂C₆F₅ and C₆F₅CF₂I?N(Me)₂CH₂CH₂(Me)₂N?ICF₂C₆F₅, respectively, have been generated from the solution of heptafluorobenzyl iodide 1 and N,N,N^′,N^′-tetramethylethylenediamine 2 in dichloromethane. Their structures have been characterized by X-ray diffraction analysis, NMR and IR spectroscopy. Intermolecular N?I halogen bond and F?H hydrogen bond are revealed to be the driving forces for their formation.     

Construction of new [2]pseudorotaxanes by hydrogen bonding assembly of macrocyclic tetrathiolactam with amides and an ester

Thionation of a macrocyclic tetralactam gave a new macrocyclic tetrathiolactam. [2]Pseudorotaxanes constructed from the macrocycle with diamides and a diester as a neutral guest have been prepared by a facile threading process. Molecular structures and hydrogen bonding association properties of the [2]pseudorotaxanes were characterized by X-ray crystallography and ¹H NMR spectroscopy.     

Ab Initio Calculations on Halogen Bond Between N——Br and Electron-donating Groups

Ab initio calculations of complexes formed between N-bromosuccinimide and a series of electron-donating groups were performed at the level of MP2/Lanl2DZ to gain a deeper insight into the nature of the N—Br halogen bonding. For the small complexes, H3C—Br…NH3 and H2N—Br…NH3, the primary calculation has demonstrated that the N—Br in H2N—Br…NH3 can form a much stronger halogen-bonding complex than the C—Br. A comparison of neutral hydrogen bond complex series reveals that the electron-donating capacities of the atoms decrease in the order, N>O>S; O(sp3)>O(sp2), which is adequate for the C—Br halogen bonding. Interaction energies, in conjunction with the geometrical parameters show that the affinitive capacity of trihalide anions X-3 with N-bromosuccinimide are markedly lower than that of the corresponding X- with N-bromosuccinimide, even lower than those of neutral molecules with N-bromosuccinimide. AIM analyses further confirmed the above results.     

Recent advances in acetylene-based helical oligomers and polymers: Synthesis,structures, and properties

In this review, we describe the recent advances in the chemistry of helical polymers and oligomers containing acetylene units in the main chain. Owing to their great benefits such as high availability and handleability, good reactivity, rigidity, linearity, and low bulkiness, acetylene units have been utilized and incorporated in helical folding oligomers and polymers such as oligo- and poly(m-phenylene ethynylene)s. General synthetic methods as well as the structures, functions, and properties of acetylene-based helical oligomers and polymers are discussed by focusing on recent examples from 2009 to 2017.     

Acid-induced conformational alteration of cis-preferential aromatic amides bearing N-methyl-N-(2-pyridyl) moiety

A series of cis-preferential aromatic N-methyl amides was designed and synthesized, and acid-induced conformational alteration of these compounds was investigated by means of NMR measurements in solution and X-ray crystal structure analysis. Compounds with a terminal N-methyl-N-(2-pyridyl) amide unit showed acid-induced conformational change from cis to trans, while those with a terminal N-methyl-2-pyridinecarboxamide unit showed a change of the carbonyl orientation from anti to syn with retention of cis conformation.     

Synthesis and studies of crowned dipyrromethenes based macrocycles

Three different meso-substituted new type of crowned dipyrromethene macrocycles were synthesized in decent yields over a sequence of four simple reaction steps using readily available precursors. The macrocycles were thoroughly characterized by HRMS as well as 1D and 2D NMR spectroscopic techniques and the structures of one of the macrocyles in its neutral form and protonated form were determined by X-ray crystallography. The crystal analysis indicated that the macrocycle was distorted in both neutral and protonated forms owing to the presence of flexible aliphatic ether chain. Absorption and electrochemical studies indicated that the properties of macrocycles were dependent on type of aryl group present at the meso-position of dipyrrin moiety of crowned dipyrromethene macrocycle. The preliminary studies indicated that the crowned dipyrromethene macrocycles can act as specific colorimetric optical sensor for Cu²⁺ ion.     

Complexation of two macrocycles for amide,saccharide, and halide derivatives: the capacity of 1,2,3-triazole as hydrogen and halogen bonding acceptors

Two 1,2,3-triazole- and amide-incorporated macrocycles have been prepared by 1,3-dipolar cycloaddition of the corresponding dialkyne and diazide precursors. Intramolecular C–H?O hydrogen bonding is introduced to lock the C⁵–H atoms of the 1,2,3-triazole rings. The binding of the two macrocycles to amide, monosaccharide, and halide derivatives in chloroform or dichloromethane has been investigated. It is revealed that the amide units dominate their binding toward the amide and monosaccharide guests through forming intermolecular hydrogen bonding and 1,2,3-triazole is as weak as an intermolecular hydrogen bonding acceptor, but it forms intermolecular halogen bonding when cooperative effect exists.